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Detailed information for vg0143242911:

Variant ID: vg0143242911 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 43242911
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGGCGGGCGTCGGTGGCCACCGTTTTTTTTTCAATTTTTTTCCATGGCTATTGCTAACCGAATCGGATTGTGTGTGGACGAAAATTAGATGTGATGAC[C/T]
GGAAAAATACGAATATTTATATTAGTTATAGATTTGTTTCGATCTTGGAGTCGTTTTCTTCAACGTGTGGTTCCTCCGCTGTGCTGCTTCCTTTTCCTCC

Reverse complement sequence

GGAGGAAAAGGAAGCAGCACAGCGGAGGAACCACACGTTGAAGAAAACGACTCCAAGATCGAAACAAATCTATAACTAATATAAATATTCGTATTTTTCC[G/A]
GTCATCACATCTAATTTTCGTCCACACACAATCCGATTCGGTTAGCAATAGCCATGGAAAAAAATTGAAAAAAAAACGGTGGCCACCGACGCCCGCCTCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.20% 17.80% 0.06% 0.00% NA
All Indica  2759 70.00% 29.90% 0.11% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 67.90% 32.10% 0.00% 0.00% NA
Indica II  465 79.60% 20.20% 0.22% 0.00% NA
Indica III  913 64.50% 35.40% 0.11% 0.00% NA
Indica Intermediate  786 72.30% 27.60% 0.13% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0143242911 C -> T LOC_Os01g74650.1 upstream_gene_variant ; 4896.0bp to feature; MODIFIER silent_mutation Average:92.714; most accessible tissue: Zhenshan97 flag leaf, score: 99.754 N N N N
vg0143242911 C -> T LOC_Os01g74660.1 upstream_gene_variant ; 1275.0bp to feature; MODIFIER silent_mutation Average:92.714; most accessible tissue: Zhenshan97 flag leaf, score: 99.754 N N N N
vg0143242911 C -> T LOC_Os01g74650.2 upstream_gene_variant ; 4896.0bp to feature; MODIFIER silent_mutation Average:92.714; most accessible tissue: Zhenshan97 flag leaf, score: 99.754 N N N N
vg0143242911 C -> T LOC_Os01g74650.3 upstream_gene_variant ; 4405.0bp to feature; MODIFIER silent_mutation Average:92.714; most accessible tissue: Zhenshan97 flag leaf, score: 99.754 N N N N
vg0143242911 C -> T LOC_Os01g74670.1 downstream_gene_variant ; 4154.0bp to feature; MODIFIER silent_mutation Average:92.714; most accessible tissue: Zhenshan97 flag leaf, score: 99.754 N N N N
vg0143242911 C -> T LOC_Os01g74650-LOC_Os01g74660 intergenic_region ; MODIFIER silent_mutation Average:92.714; most accessible tissue: Zhenshan97 flag leaf, score: 99.754 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0143242911 C T -0.1 -0.07 -0.04 -0.06 -0.07 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0143242911 NA 3.07E-06 mr1215 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0143242911 NA 9.37E-06 mr1909 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0143242911 NA 8.04E-06 mr1960 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0143242911 1.63E-07 1.60E-07 mr1974 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0143242911 5.52E-07 3.43E-09 mr1974 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251